rapodaca / dialect

Documenting a subset of the SMILES language.
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Reversed Partial Parity Bond #23

Closed rapodaca closed 3 years ago

rapodaca commented 3 years ago

Conformation describes a convention for working with partial parity bonds (BBPs). It assumes that bonds are encoded left-to-right. In other words, target always succeeds source.

This works under the assumption that the graph has no cycles. If one exists, then the edge that bites back can be forward (target succeeds), reverse (target precedes), or both. This case leads to incorrect selection of neighbor quadrant.

Whatever solution is chosen must account for the apparent dual state of the central PPB in hexadiene (C/C=C/C=C/C).

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